CAP - Consortium to Alleviate PTSD- STVHCS Biomarkers & Genomics Core

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Biomarkers and Genomics Core The primary objectives of the Biomarkers and Genomics Core are to (1) support the efforts of STRONG STAR- CAP studies with biomarker or genomic components involving the collection and analysis of biological and physiological specimens; (2) to centralize the collection, processing, storage, and analysis of samples; and (3) to maintain a biospecimen repository linkable with clinical data through the overall Consortium data repository; (4) facilitate the collection of human postmortem tissue in order to accelerate PTSD biomarker discovery; and (5) link with expertise to facilitate the translation of biomarker discovery into diagnostic and prognostic panels (e.g., Lee Hood and the Institute for Systems Biology). The Biomarkers and Genomics Core will make use of an extensive infrastructure developed as part of STRONG STAR over the last four years for accelerating biomarker studies of PTSD. In addition, through our partnering arrangement with the NCPTSD, we have expanded to include the resources and expertise available at Yale University as directed by Dr. Gelertner. The Biomarkers and Genomics Core has developed extensive standardized procedures for collecting blood specimens for use in DNA, RNA, and plasma base protein and microRNA research. Standard operating procedures have been developed for PAXgene-based DNA/RNA collection and automated extraction procedures to optimize the quantity and quality of the sample yields for downstream applications. In addition, we have refined the methods for plasma collection for downstream proteomic and microRNA applications that will facilitate the proposed work by Drs. K. Young and L. Hood (see Project 3). The Core is housed in 200,000 square feet of a state-of-the-art research facility, the South Texas Research Facility, located at UTHSCSA. Core analytic infrastructure includes Illumina iScan with Tecan automation (microarray), Illumina MiSeq (small- scale NextGen sequencing), Illumina HiSeq (large-scale NextGen sequencing), Fluidigm Biomark HD (real- time PCR), Qiagen Pyromark Q96 MD (targeted sequencing/methylation), and Luminex FlexMap 3D (multiplex analyte analysis). In addition to state-of-the-art translational technologies for downstream analyses, the Biomarkers and Genomics Core also houses the STRONG STAR-CAP biorepository. The biorepository has the capacity for housing 24 freezers (-80/-130) in a secure card-accessed room. All freezers are monitored real- time on the UTHSCSA network with temperature notifications delivered via text message, e-mail, and by phone and 1-minute epoch freezer logs maintained on a virtual server. All samples are extensively catalogued using Freezerworks to track samples from their origin through their associated derivatives. Working with the Data, Statistics, and Repository Core, we are currently developing systems integrating the biorepository information in Freezerworks with the repository dataset to facilitate linking clinical and biomarker data with sample availability. In STRONG STAR-CAP, we have partnered with the Southwest Brain Bank at UTHSCSA (P. Thompson & D. Cruz) to add to the collection of human postmortem tissue (currently 180 brains overall and 10 brains from persons with PTSD) to significantly expand the availability of PTSD brains (by targeting the large VA population in San Antonio) to support the proposed biomarker discovery in Project 3 (Williamson & Hood) as well as for future studies supported by the Consortium. In addition, the Biomarkers and Genomics Core will also facilitate the collection of blood specimens in VA studies (~400/year) being collected by Dr. Acierno and colleagues.